On Thu, Apr 11, 2013 at 6:52 AM, Ahmet yıldırım <ahmedo...@gmail.com> wrote:
> Dear Justin, > > I copied to gmx.ff it. You know the tip5p shows the general shape of the > 5-site water models but the spc shows the general shape of the 3-site water > models. Therefore I need tip5p.itp. > Is there going to be a protein in the system, as well? If so, gmx.ff is a poor choice and I would still maintain that despite any possible improvement in water model (and none of them are perfect), it's not a proper combination. If you're simulating pure water, the choice of parent force field is largely irrelevant. > How can you get it? > > I have no idea why your tip5p.itp is wrong. The atom type should be MW for both LP1 and LP2, as I said before. Fix the atom types and the problem should go away. -Justin > > 2013/4/11 Justin Lemkul <jalem...@vt.edu> > > > On Thu, Apr 11, 2013 at 1:56 AM, Ahmet yıldırım <ahmedo...@gmail.com> > > wrote: > > > > > Dear users, > > > > > > I am trying MD simulation of tip5p water model. I am getting Fatal > > > Error:Atomtype LP1 not found. > > > There isnt LP in atomtypes.atp file. Which one corresponds to LP1 and > LP2 > > > atoms in atomtypes.atp file? > > > (I am using Gromacs 4.5.5) > > > > > > > > > usr/share/gromacs/top/gmx.ff/tip5p.itp > > > ... > > > [ atoms ] > > > ; id at type res nr residu name at name cg nr charge > > > 1 OW 1 SOL OW 1 0 > > > 2 HW1 1 SOL HW1 1 > > > 0.241 > > > 3 HW2 1 SOL HW2 1 > > 0.241 > > > 4 LP1 1 SOL LP1 1 > > -0.241 > > > 5 LP2 1 SOL LP2 1 > > -0.241 > > > .... > > > > > > > > It looks like someone has erroneously modified your files. The TIP5P > model > > should not be included in gmx.ff (Gromos force fields should be used with > > SPC), and the atom type for both LP1 and LP2 should be MW. > > > > -Justin > > > > -- > > > > ======================================== > > > > Justin A. Lemkul, Ph.D. > > Research Scientist > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) > > 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > ======================================== > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > Ahmet Yıldırım > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists